5Z3N

Structure of large fragment of DNA Polymerase I from Thermus aquaticus Host-Guest complex with the unnatural base 5fC pair with dA


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4DFK 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1EVAPORATION7293.150.05 M sodium cacodylate (pH 7.0), 0.2 M ammonium acetate, 0.01 M magnesium acetate, 24% PEG 8000
Crystal Properties
Matthews coefficientSolvent content
2.1843.67

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 107.947α = 90
b = 107.947β = 90
c = 90.121γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 130 mm2017-12-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U10.9793SSRFBL17U1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.9193.4999.818.696.442010
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.911.94

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4DFK1.9193.4842010221592.940.185680.18340.22933RANDOM26.317
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
-0.18-0.09-0.180.59
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.163
r_dihedral_angle_4_deg16.501
r_dihedral_angle_3_deg14.297
r_dihedral_angle_1_deg9.287
r_long_range_B_refined5.794
r_long_range_B_other5.794
r_angle_refined_deg1.55
r_angle_other_deg1.152
r_scangle_other0.791
r_mcangle_it0.707
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.163
r_dihedral_angle_4_deg16.501
r_dihedral_angle_3_deg14.297
r_dihedral_angle_1_deg9.287
r_long_range_B_refined5.794
r_long_range_B_other5.794
r_angle_refined_deg1.55
r_angle_other_deg1.152
r_scangle_other0.791
r_mcangle_it0.707
r_mcangle_other0.707
r_scbond_it0.467
r_scbond_other0.467
r_mcbond_it0.396
r_mcbond_other0.394
r_chiral_restr0.091
r_bond_refined_d0.01
r_gen_planes_refined0.009
r_bond_other_d0.002
r_gen_planes_other0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4278
Nucleic Acid Atoms568
Solvent Atoms498
Heterogen Atoms64

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
SCALEPACKdata scaling
PHASERphasing